FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: Q86KY

Calculation Name: 6WTC-CD-Xray160

Preferred Name:

Target Type:

Ligand Name: acetic acid

ligand 3-letter code: ACY

PDB ID: 6WTC

Chain ID: CD

ChEMBL ID:

UniProt ID: P0DTD1

Base Structure: X-ray

Registration Date: 2020-09-23

Reference: K. Kato Y. Handa, Y. Kawashima, K. Fukuzawa, C. Watanabe, T. Honma, , To be published

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHL
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Selected crystal waters in PDB
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge None
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2078748.012269
FMO2-HF: Nuclear repulsion 2001543.951338
FMO2-HF: Total energy -77204.060932
FMO2-MP2: Total energy -77421.348388


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(C:0:ALA )


Summations of interaction energy for fragment #1(C:0:ALA )
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
16.20521.0440.526-2.039-3.328-0.012
Interaction energy analysis for fragmet #1(C:0:ALA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.883 / q_NPA : 0.931
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3C2LYS 11.0641.0412.89446.60049.4900.076-1.310-1.657-0.006
4C3MET 0-0.031-0.0142.6515.6227.2410.451-0.633-1.437-0.006
5C4SER 0-0.0080.0094.3979.0579.249-0.001-0.047-0.1450.000
6C5ASP -1-0.864-0.9236.662-30.669-30.6690.0000.0000.0000.000
7C6VAL 0-0.0020.0006.6804.2724.2720.0000.0000.0000.000
8C7LYS 10.8950.9557.21637.04437.0440.0000.0000.0000.000
9C8CYS 0-0.012-0.00110.4053.6053.6050.0000.0000.0000.000
10C9THR 00.012-0.01311.8582.4182.4180.0000.0000.0000.000
11C10SER 0-0.0140.00413.0731.9571.9570.0000.0000.0000.000
12C11VAL 00.0560.03214.6661.4701.4700.0000.0000.0000.000
13C12VAL 00.0030.00416.5771.4921.4920.0000.0000.0000.000
14C13LEU 00.0000.00917.3931.0611.0610.0000.0000.0000.000
15C14LEU 00.0060.00819.0750.8960.8960.0000.0000.0000.000
16C15SER 00.0200.00420.9121.0891.0890.0000.0000.0000.000
17C16VAL 00.008-0.01022.1840.7890.7890.0000.0000.0000.000
18C17LEU 00.0350.01422.4020.7560.7560.0000.0000.0000.000
19C18GLN 0-0.0200.00525.1220.1430.1430.0000.0000.0000.000
20C19GLN 0-0.089-0.03726.8750.8890.8890.0000.0000.0000.000
21C20LEU 0-0.062-0.01926.6900.5080.5080.0000.0000.0000.000
22C21ARG 10.9050.95629.9549.5479.5470.0000.0000.0000.000
23C22VAL 00.0780.03327.3560.3070.3070.0000.0000.0000.000
24C23GLU -1-0.891-0.94929.182-10.795-10.7950.0000.0000.0000.000
25C24SER 0-0.086-0.03130.3850.2650.2650.0000.0000.0000.000
26C25SER 00.0050.01331.7180.3380.3380.0000.0000.0000.000
27C26SER 00.0690.01931.330-0.365-0.3650.0000.0000.0000.000
28C27LYS 10.9550.96830.7738.5858.5850.0000.0000.0000.000
29C28LEU 00.0330.02327.426-0.308-0.3080.0000.0000.0000.000
30C29TRP 00.0740.03024.779-0.547-0.5470.0000.0000.0000.000
31C30ALA 00.0110.00725.868-0.488-0.4880.0000.0000.0000.000
32C31GLN 00.0070.00024.993-0.627-0.6270.0000.0000.0000.000
33C32CYS 00.0100.01122.357-0.693-0.6930.0000.0000.0000.000
34C33VAL 00.0160.01121.059-0.848-0.8480.0000.0000.0000.000
35C34GLN 0-0.033-0.00320.390-1.088-1.0880.0000.0000.0000.000
36C35LEU 00.0000.00618.493-0.699-0.6990.0000.0000.0000.000
37C36HIS 00.005-0.00616.748-1.642-1.6420.0000.0000.0000.000
38C37ASN 0-0.0060.00515.679-1.491-1.4910.0000.0000.0000.000
39C38ASP -1-0.822-0.91515.445-17.770-17.7700.0000.0000.0000.000
40C39ILE 0-0.051-0.02211.122-1.849-1.8490.0000.0000.0000.000
41C40LEU 0-0.038-0.02910.885-3.115-3.1150.0000.0000.0000.000
42C41LEU 0-0.064-0.03011.083-1.637-1.6370.0000.0000.0000.000
43C42ALA 00.0230.0389.424-0.017-0.0170.0000.0000.0000.000
44C43LYS 10.9110.9598.63521.26421.2640.0000.0000.0000.000
45C44ASP -1-0.862-0.9486.697-34.332-34.3320.0000.0000.0000.000
46C45THR 0-0.015-0.0433.834-1.983-1.8450.000-0.049-0.0890.000
47C46THR 00.0030.0086.5811.3071.3070.0000.0000.0000.000
48C47GLU -1-0.850-0.90410.072-19.876-19.8760.0000.0000.0000.000
49C48ALA 0-0.025-0.0228.4821.4951.4950.0000.0000.0000.000
50C49PHE 0-0.022-0.0427.0570.1990.1990.0000.0000.0000.000
51C50GLU -1-0.883-0.92711.605-18.070-18.0700.0000.0000.0000.000
52C51LYS 10.9320.96414.17518.83918.8390.0000.0000.0000.000
53C52MET 0-0.042-0.02012.1231.5111.5110.0000.0000.0000.000
54C53VAL 00.0230.01815.1091.0961.0960.0000.0000.0000.000
55C54SER 0-0.0110.00517.5740.7850.7850.0000.0000.0000.000
56C55LEU 00.0010.00517.1910.8010.8010.0000.0000.0000.000
57C56LEU 0-0.002-0.01317.7920.6560.6560.0000.0000.0000.000
58C57SER 0-0.008-0.00719.9470.9090.9090.0000.0000.0000.000
59C58VAL 00.0300.00522.8580.6850.6850.0000.0000.0000.000
60C59LEU 0-0.012-0.01022.2780.4970.4970.0000.0000.0000.000
61C60LEU 0-0.047-0.02521.9090.4170.4170.0000.0000.0000.000
62C61SER 0-0.0190.01225.6500.4630.4630.0000.0000.0000.000
63C62MET 0-0.085-0.03628.3290.3330.3330.0000.0000.0000.000
64C63GLN 00.0590.02330.3100.1060.1060.0000.0000.0000.000
65C64GLY 0-0.0050.00033.0360.1770.1770.0000.0000.0000.000
66C65ALA 0-0.044-0.00430.0650.0990.0990.0000.0000.0000.000
67C66VAL 0-0.035-0.03126.596-0.062-0.0620.0000.0000.0000.000
68C67ASP -1-0.868-0.94429.833-9.580-9.5800.0000.0000.0000.000
69C68ILE 00.0320.01625.201-0.274-0.2740.0000.0000.0000.000
70C69ASN 00.0800.00926.563-0.635-0.6350.0000.0000.0000.000
71C70LYS 10.8600.95328.4439.3049.3040.0000.0000.0000.000
72C71LEU 0-0.052-0.01424.655-0.150-0.1500.0000.0000.0000.000
73C72CYS -1-0.943-0.94323.326-13.736-13.7360.0000.0000.0000.000
74D78ASP 00.0250.00037.116-0.147-0.1470.0000.0000.0000.000
75D79LYS 11.0551.01133.2339.3939.3930.0000.0000.0000.000
76D80ARG 11.0091.01032.4769.4729.4720.0000.0000.0000.000
77D81ALA 00.0550.03932.044-0.333-0.3330.0000.0000.0000.000
78D82LYS 10.9750.98731.9208.6808.6800.0000.0000.0000.000
79D83VAL 00.0280.01828.114-0.277-0.2770.0000.0000.0000.000
80D84THR 00.0170.01027.590-0.431-0.4310.0000.0000.0000.000
81D85SER 0-0.0040.00827.047-0.497-0.4970.0000.0000.0000.000
82D86ALA 00.0200.01326.177-0.329-0.3290.0000.0000.0000.000
83D87MET 0-0.0090.00822.522-0.622-0.6220.0000.0000.0000.000
84D88GLN 00.005-0.01122.144-0.624-0.6240.0000.0000.0000.000
85D89THR 00.0460.02622.584-0.332-0.3320.0000.0000.0000.000
86D90MET 0-0.041-0.00918.621-0.870-0.8700.0000.0000.0000.000
87D91LEU 00.0190.00917.285-1.057-1.0570.0000.0000.0000.000
88D92PHE 00.0640.01417.483-1.102-1.1020.0000.0000.0000.000
89D93THR 0-0.038-0.00717.440-0.334-0.3340.0000.0000.0000.000
90D94MET 0-0.070-0.03712.300-0.756-0.7560.0000.0000.0000.000
91D95LEU 00.0110.00213.409-1.774-1.7740.0000.0000.0000.000
92D96ARG 10.9600.98614.33614.75914.7590.0000.0000.0000.000
93D97LYS 10.9110.95711.53422.93522.9350.0000.0000.0000.000
94D98LEU 0-0.100-0.0458.623-2.299-2.2990.0000.0000.0000.000
95D99ASP -1-0.899-0.93310.237-23.074-23.0740.0000.0000.0000.000
96D100ASN 0-0.021-0.00910.7820.6590.6590.0000.0000.0000.000
97D101ASP -1-0.825-0.91112.569-18.313-18.3130.0000.0000.0000.000
98D102ALA 0-0.024-0.01215.0491.2381.2380.0000.0000.0000.000
99D103LEU 0-0.034-0.03512.8910.9370.9370.0000.0000.0000.000
100D104ASN 00.0450.01916.2630.7430.7430.0000.0000.0000.000
101D105ASN 0-0.0400.00018.1961.1331.1330.0000.0000.0000.000
102D106ILE 00.0220.00219.1090.6780.6780.0000.0000.0000.000
103D107ILE 0-0.016-0.00518.0310.5320.5320.0000.0000.0000.000
104D108ASN 0-0.041-0.04621.5580.6350.6350.0000.0000.0000.000
105D109ASN 00.0220.01723.9390.8410.8410.0000.0000.0000.000
106D110ALA 00.0060.01125.1570.5080.5080.0000.0000.0000.000
107D111ARG 10.8150.92223.55112.98712.9870.0000.0000.0000.000
108D112ASP -1-0.890-0.93627.919-10.629-10.6290.0000.0000.0000.000
109D113GLY 0-0.030-0.00730.0360.3930.3930.0000.0000.0000.000
110D114CYS 0-0.063-0.01328.9290.1960.1960.0000.0000.0000.000
111D115VAL 00.0210.02527.804-0.562-0.5620.0000.0000.0000.000
112D116PRO 0-0.042-0.01525.2880.2810.2810.0000.0000.0000.000
113D117LEU 00.019-0.00628.4590.1110.1110.0000.0000.0000.000
114D118ASN 0-0.050-0.02528.7570.3690.3690.0000.0000.0000.000
115D119ILE 0-0.023-0.01323.494-0.261-0.2610.0000.0000.0000.000
116D120ILE 00.0370.03221.9330.3250.3250.0000.0000.0000.000
117D121PRO 0-0.0260.00922.617-0.687-0.6870.0000.0000.0000.000
118D122LEU 00.003-0.02918.036-0.219-0.2190.0000.0000.0000.000
119D123THR 0-0.0210.00221.865-0.195-0.1950.0000.0000.0000.000
120D124THR 00.0560.01224.5720.1350.1350.0000.0000.0000.000
121D125ALA 00.0000.00627.1390.2200.2200.0000.0000.0000.000
122D126ALA 0-0.044-0.00427.0300.3310.3310.0000.0000.0000.000
123D127LYS 10.9740.96829.1489.0509.0500.0000.0000.0000.000
124D128LEU 0-0.017-0.00526.348-0.375-0.3750.0000.0000.0000.000
125D129MET 0-0.0220.00529.9100.3080.3080.0000.0000.0000.000
126D130VAL 00.0220.00128.469-0.359-0.3590.0000.0000.0000.000
127D131VAL 0-0.0100.00931.3200.3330.3330.0000.0000.0000.000
128D132ILE 00.014-0.00431.799-0.335-0.3350.0000.0000.0000.000
129D133PRO 0-0.001-0.00232.9890.3330.3330.0000.0000.0000.000
130D134ASP -1-0.785-0.90135.445-8.787-8.7870.0000.0000.0000.000
131D135TYR 00.0630.01036.367-0.187-0.1870.0000.0000.0000.000
132D136ASN 0-0.070-0.04134.939-0.024-0.0240.0000.0000.0000.000
133D137THR 00.0190.00830.704-0.327-0.3270.0000.0000.0000.000
134D138TYR 00.0490.02032.180-0.226-0.2260.0000.0000.0000.000
135D139LYS 10.9310.96333.7938.5118.5110.0000.0000.0000.000
136D140ASN 0-0.040-0.01029.5770.0340.0340.0000.0000.0000.000
137D141THR 0-0.069-0.03228.136-0.378-0.3780.0000.0000.0000.000
138D142CYS 0-0.041-0.00230.058-0.184-0.1840.0000.0000.0000.000
139D143ASP -1-0.912-0.94032.737-9.079-9.0790.0000.0000.0000.000
140D144GLY 00.0130.01234.345-0.063-0.0630.0000.0000.0000.000
141D145THR 0-0.009-0.01636.128-0.056-0.0560.0000.0000.0000.000
142D146THR 0-0.024-0.00130.709-0.245-0.2450.0000.0000.0000.000
143D147PHE 00.0400.00128.3820.0260.0260.0000.0000.0000.000
144D148THR 0-0.001-0.01024.863-0.441-0.4410.0000.0000.0000.000
145D149TYR 00.0200.01124.4620.0500.0500.0000.0000.0000.000
146D150ALA 00.0010.00520.242-0.210-0.2100.0000.0000.0000.000
147D151SER 0-0.035-0.03617.103-0.384-0.3840.0000.0000.0000.000
148D152ALA 0-0.0040.01520.015-0.370-0.3700.0000.0000.0000.000
149D153LEU 00.0340.01622.5130.4130.4130.0000.0000.0000.000
150D154TRP 0-0.026-0.03423.5430.0110.0110.0000.0000.0000.000
151D155GLU -1-0.919-0.96728.843-9.595-9.5950.0000.0000.0000.000
152D156ILE 0-0.019-0.02332.4990.0670.0670.0000.0000.0000.000
153D157GLN 0-0.113-0.05734.7970.3910.3910.0000.0000.0000.000
154D158GLN 0-0.038-0.03437.4360.2400.2400.0000.0000.0000.000
155D159VAL 00.0310.01737.385-0.301-0.3010.0000.0000.0000.000
156D160VAL 0-0.036-0.00439.6200.2280.2280.0000.0000.0000.000
157D161ASP -1-0.801-0.90940.601-7.235-7.2350.0000.0000.0000.000
158D162ALA 0-0.015-0.00542.445-0.032-0.0320.0000.0000.0000.000
159D163ASP -1-0.987-0.99643.383-6.488-6.4880.0000.0000.0000.000
160D164SER 0-0.082-0.03643.8130.0550.0550.0000.0000.0000.000
161D165LYS 10.9030.95444.8676.4556.4550.0000.0000.0000.000
162D166ILE 0-0.031-0.01543.180-0.133-0.1330.0000.0000.0000.000
163D167VAL 00.0190.01942.6680.1410.1410.0000.0000.0000.000
164D168GLN 0-0.037-0.01143.138-0.308-0.3080.0000.0000.0000.000
165D169LEU 00.030-0.00839.053-0.021-0.0210.0000.0000.0000.000
166D170SER 0-0.059-0.02542.385-0.056-0.0560.0000.0000.0000.000
167D171GLU -1-0.865-0.93145.262-6.720-6.7200.0000.0000.0000.000
168D172ILE 00.0030.02239.4560.0300.0300.0000.0000.0000.000
169D173SER 00.0160.00741.729-0.137-0.1370.0000.0000.0000.000
170D174MET 0-0.0060.00542.371-0.061-0.0610.0000.0000.0000.000
171D175ASP -1-0.972-0.98843.817-6.376-6.3760.0000.0000.0000.000
172D176ASN 00.0430.02146.5640.2480.2480.0000.0000.0000.000
173D177SER 0-0.001-0.02442.586-0.058-0.0580.0000.0000.0000.000
174D178PRO 0-0.027-0.01544.647-0.056-0.0560.0000.0000.0000.000
175D179ASN 0-0.056-0.02446.7380.1270.1270.0000.0000.0000.000
176D180LEU 0-0.037-0.00643.1140.0550.0550.0000.0000.0000.000
177D181ALA 00.0090.01045.414-0.012-0.0120.0000.0000.0000.000
178D182TRP 0-0.0130.00837.741-0.248-0.2480.0000.0000.0000.000
179D183PRO 0-0.026-0.02737.4560.1140.1140.0000.0000.0000.000
180D184LEU 00.0120.01537.8810.1300.1300.0000.0000.0000.000
181D185ILE 00.0040.00335.574-0.308-0.3080.0000.0000.0000.000
182D186VAL 00.0160.02632.5570.2500.2500.0000.0000.0000.000
183D187THR 0-0.009-0.01433.750-0.271-0.2710.0000.0000.0000.000
184D188ALA 00.0030.00030.8960.1630.1630.0000.0000.0000.000
185D189LEU 0-0.035-0.01530.831-0.103-0.1030.0000.0000.0000.000
186D190ARG 10.8500.94720.41414.24214.2420.0000.0000.0000.000
187D191ALA 00.0790.04927.1140.2980.2980.0000.0000.0000.000
188D192ASN 0-0.067-0.05725.660-0.124-0.1240.0000.0000.0000.000
189D193SER -1-0.946-0.95921.475-14.430-14.4300.0000.0000.0000.000
190C401HOH 0-0.043-0.03722.123-0.105-0.1050.0000.0000.0000.000
191C402HOH 0-0.043-0.04020.3140.3180.3180.0000.0000.0000.000
192C403HOH 0-0.036-0.02919.9890.0070.0070.0000.0000.0000.000
193C406HOH 0-0.007-0.01321.0780.0570.0570.0000.0000.0000.000
194C407HOH 00.006-0.01023.009-0.125-0.1250.0000.0000.0000.000
195C408HOH 00.001-0.01026.784-0.091-0.0910.0000.0000.0000.000
196C409HOH 0-0.010-0.01230.140-0.065-0.0650.0000.0000.0000.000
197C410HOH 0-0.004-0.00223.1860.1930.1930.0000.0000.0000.000
198C411HOH 00.0040.00130.594-0.112-0.1120.0000.0000.0000.000
199C415HOH 0-0.008-0.00922.3960.2670.2670.0000.0000.0000.000
200C416HOH 0-0.017-0.01225.8600.1890.1890.0000.0000.0000.000
201D201HOH 00.0270.00544.011-0.038-0.0380.0000.0000.0000.000
202D202HOH 0-0.024-0.02741.747-0.035-0.0350.0000.0000.0000.000
203D203HOH 00.0290.02022.2780.0950.0950.0000.0000.0000.000
204D204HOH 00.0180.02218.9800.1830.1830.0000.0000.0000.000
205D205HOH 0-0.012-0.03725.438-0.159-0.1590.0000.0000.0000.000
206D206HOH 0-0.022-0.01814.203-0.423-0.4230.0000.0000.0000.000
207D207HOH 0-0.027-0.02726.8310.1680.1680.0000.0000.0000.000
208D208HOH 00.0190.01544.350-0.064-0.0640.0000.0000.0000.000
209D209HOH 00.0000.00530.222-0.123-0.1230.0000.0000.0000.000
210D210HOH 00.0200.01822.103-0.177-0.1770.0000.0000.0000.000
211D211HOH 00.013-0.00725.619-0.134-0.1340.0000.0000.0000.000
212D212HOH 0-0.031-0.02430.0000.1500.1500.0000.0000.0000.000
213D214HOH 0-0.006-0.01138.145-0.064-0.0640.0000.0000.0000.000
214D216HOH 00.0330.02548.771-0.001-0.0010.0000.0000.0000.000
215D217HOH 0-0.019-0.01631.7340.0510.0510.0000.0000.0000.000
216D218HOH 0-0.007-0.00244.806-0.023-0.0230.0000.0000.0000.000
217D220HOH 0-0.025-0.01324.042-0.008-0.0080.0000.0000.0000.000